Development and Transfer Analysis of SSR in Dendrobium

To date,only 100 SSR markers in Dendrobium have been developed,which are far from sufficient for research applications.To develop molecular markers,we mined SSR of Dendrobium from public nucleotide data through bioinformation methods.Some 1343 Uni-DNA sequences were assembled from the 3599 DNA sequences of Dendrobium from GenBank.By scanning the Uni-DNA sequences,283 SSRs were distributed in 205 Uni-DNA sequences,with an average frequency of 1 SSR per 2815 bp.Sequence alignment indicated that 86 of the 205 SSR-DNA sequences had already been used to design primers.In this study,76 primer pairs were designed from the remaining 119 sequences for transferability analysis among 32 Dendrobium species.Results showed that 47 primer pairs were amplified effectively with transfer rates ranging from 51.1% to 95.7% (average 75.9%).Of which,46 primer pairs were able to detect polymorphism among the Dendrobium species with 2-8 alleles (average 4.0 alleles).Ten pairs of polymorphic primers were selected to detect polymorphism in 60 accessions of D.officinale,and 2-5 alleles (average 3.4 alleles) were found per SSR locus.Based on the SSR amplification pattern,the 60 accessions of D.officinale were clustered into five clusters,and phenotypes were closer within clusters than between clusters.The sequencing of the amplified fragment of DM121 revealed that allele variation within D.officinale was attributed mainly to the variation of SSR repeat numbers,whereas allele variations among Dendrobium species were also caused by a single base indel and substitution in the microsatellite flanking region.